First off, I'm 5'10" and I ride a 54. Over the years, I've been fit by a number of different shops on a number of different systems/calculators, and I've always come up with a 54. I own more than a dozen top end bikes sold to me by one of the best shops in the NE, and a few made by King Eddy after his factory confirmed my measurements. There are no absolutes or fixed rules when it comes to fit. Generally. most fit systems/calculators will get you in the ballpark of the right frame size. Then you need to work with your LBS to to tweak it.
Listen to your body. If after three months, you think you are too stretched out, then you probably are. Being on a road machine doesn't mean that you should automatically feel uncomfortable. If you have already swapped out the stem and you have your seat jammed forward on the seatpost, your LBS should be getting the idea that maybe you bought the wrong size. You should speak with your LBS about the problem. Get a proper fit done before spending more money. Some shops will give you a break on a new frameset and/or help you sell your old bike. You should understand, however, that there's not much of a markup on complete bikes, and what you have now is a used bike worth about 50-60% of what you paid for it. Best of luck!